SMTL ID : 7rpj.1

Cryo-EM structure of murine Dispatched NNN mutant

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

5 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 3 residues within 4Å: Chain A: N.306, S.308, G.310 No protein-ligand interaction detected (PLIP) NAG.2: 3 residues within 4Å: Chain A: Q.661, K.662, N.665 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.661 NAG.3: 3 residues within 4Å: Chain A: D.744, I.745, N.746 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.746 NAG.4: 3 residues within 4Å: Chain A: H.218, N.221, T.223 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.221, A:T.223 NAG.5: 2 residues within 4Å: Chain A: Q.117, N.193 No protein-ligand interaction detected (PLIP)

14 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.6: 4 residues within 4Å: Chain A: Y.11, Q.432, V.479 Ligands: Y01.14 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.11, A:Y.11, A:Q.432, A:V.479 Y01.7: 11 residues within 4Å: Chain A: I.343, L.346, I.347, V.350, Y.351, V.527, S.528, S.531, M.914, L.917 Ligands: Y01.19 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:I.343, A:L.346, A:I.347, A:V.350, A:Y.351, A:L.917 Hydrogen bonds: A:S.531 Y01.8: 10 residues within 4Å: Chain A: K.570, M.571, K.572, L.573, M.817, A.846, I.849, F.850, L.863, I.871 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:K.570, A:M.571, A:L.573, A:I.849, A:F.850, A:F.850, A:L.863, A:I.871 Hydrogen bonds: A:L.573 Y01.9: 5 residues within 4Å: Chain A: R.585, M.927, M.942 Ligands: Y01.12, Y01.19 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.585 Y01.10: 4 residues within 4Å: Chain A: F.534, A.916, C.946 Ligands: Y01.12 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.534, A:F.534, A:A.916 Y01.11: 4 residues within 4Å: Chain A: V.20, T.27, F.363, Y.492 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.20, A:T.27, A:F.363, A:Y.492, A:Y.492, A:Y.492 Hydrogen bonds: A:Y.492 Y01.12: 5 residues within 4Å: Chain A: L.859, T.939, C.946 Ligands: Y01.9, Y01.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.859, A:T.939 Y01.13: 5 residues within 4Å: Chain A: L.346, K.353, F.497, R.521, L.524 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.346, A:F.497, A:L.524 Salt bridges: A:K.353, A:R.521 Y01.14: 5 residues within 4Å: Chain A: Q.432, F.439, Y.475 Ligands: Y01.6, Y01.16 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.439, A:Y.475 Y01.15: 4 residues within 4Å: Chain A: F.46, Q.327, L.369, Y.466 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.46, A:F.46, A:L.369 Y01.16: 8 residues within 4Å: Chain A: L.436, F.439, F.443, L.830, W.833, R.890, F.974 Ligands: Y01.14 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.436, A:F.439, A:F.443, A:L.830 Salt bridges: A:R.890 Y01.17: 3 residues within 4Å: Chain A: L.859, L.943, A.950 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.859, A:L.943, A:A.950 Y01.18: 3 residues within 4Å: Chain A: L.29, V.476, L.477 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.29, A:L.477 Y01.19: 6 residues within 4Å: Chain A: R.585, S.587, M.925, M.927 Ligands: Y01.7, Y01.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:M.927 Hydrogen bonds: A:S.587

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, Q. et al., Dispatched uses Na + flux to power release of lipid-modified Hedgehog. Nature (2021)

Release Date

2021-10-27

Peptides

Protein dispatched homolog 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
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Protein dispatched homolog 1